polymer_dropcast_experiment_draft.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "53e1ce82",
   "metadata": {},
   "source": [
    "# Polymer dropcast experiment setup\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6179f1a2",
   "metadata": {},
   "source": [
    "#### Necessary Imports \n",
    "\n",
    "As usual, let's start by importing the necessary packages we will need to run our demo.\n",
    "\n",
    "In this case, we will also set up our matplotlib- the package we will use to visualize the beautiful art that our Rob Ross will generate as an external window."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 223,
   "id": "7b24657e-16d1-4e88-b56e-36b13f775d13",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The autoreload extension is already loaded. To reload it, use:\n",
      "  %reload_ext autoreload\n"
     ]
    }
   ],
   "source": [
    "%load_ext autoreload\n",
    "\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 224,
   "id": "938fbdb1",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ----------- Science Jubilee -------------\n",
    "from science_jubilee import Machine as Jub\n",
    "from science_jubilee.tools import Pipette\n",
    "\n",
    "# ------ Data visualization outside of the notebook ------\n",
    "import matplotlib\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1c6d3f82",
   "metadata": {},
   "source": [
    "### Jubilee platfform connection and set-up"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 225,
   "id": "18476b27",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "jubilee = Jub.Machine(address='192.168.1.2', simulated = False) "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cb6260ae",
   "metadata": {},
   "source": [
    "Before we can set up the `deck` of our `Jubilee` with all our labware, we will need to *home* **all** its axis.\n",
    "\n",
    "> Attention -- !!! **BEFORE** !!! running the next cell, make sure that NO labware is loaded onto the deck or the Tool Changer will crush into them. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 226,
   "id": "ed7d230f",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "jubilee.home_all()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "986929fb",
   "metadata": {},
   "source": [
    "### Deck preparation and labware definition \n",
    "Awesome, now that we have our machine all ready to go, we will need to load all the labware onto it both *physically* and *digitally* . \n",
    "\n",
    "* Physically: place the desired/required labware for the Demo onto the deck of your Jubilee\n",
    "* Digitally: first, we need to define our `deck`; then define and load the `labware` we want to use and indicate on which `slot` each of them was assigned to"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 227,
   "id": "97e90bef",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ---------------- Deck -------------------\n",
    "deck = jubilee.load_deck('lab_automation_deck.json')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "15cf3028",
   "metadata": {},
   "source": [
    "To run this *autonoous* color matching demo, we will need at least four types of labware:\n",
    "\n",
    "* A **Tiprack** that is suitable for the pipette you are using to transfer your liquids\n",
    "* A **Sample Labware** that will be used to collect the colors that your Rob Ross will make \n",
    "* A **Stock Labware** that will host the stock colors that your Rob Ross can mix together\n",
    "* A **trash** to collect the used tips"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 228,
   "id": "517eb33e-dfae-4bff-9dad-3cdaa114f708",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "10"
      ]
     },
     "execution_count": 228,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "deck.safe_z"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 269,
   "id": "3057dac8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "New manual offset applied to opentrons_96_tiprack_300ul\n"
     ]
    }
   ],
   "source": [
    "# -------------- Labware ------------------\n",
    "tiprack = jubilee.load_labware('opentrons_96_tiprack_300ul.json', 0)\n",
    "tiprack.load_manualOffset()\n",
    "sample_wellplate = jubilee.load_labware('falcon_48_wellplate_1500ul.json', 2) #Replace this with custom labware for samples\n",
    "#samples.load_manualOffset()\n",
    "stocks = jubilee.load_labware('20mlscintillation_12_wellplate_18000ul.json', 3)\n",
    "trash = jubilee.load_labware('agilent_1_reservoir_290ml.json', 1)\n",
    "mixing_wellplate = jubilee.load_labware('falcon_48_wellplate_1500ul.json', 4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 270,
   "id": "14501c58-6d6b-4e01-abe4-805869ea855e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "New manual offset applied to opentrons_96_tiprack_300ul\n",
      "New manual offset applied to 20mlscintillation_12_wellplate_18000ul\n"
     ]
    }
   ],
   "source": [
    "#UL = (26.5, 174.0)\n",
    "#UR = (126.6, 173.4)\n",
    "#BR = (126.5, 110.9)\n",
    "#samples.manual_offset((UL, UR, BR))\n",
    "\n",
    "UL = (29.4, 82.1)\n",
    "UR = (127, 82.1)\n",
    "BR = (127, 19.2)\n",
    "tiprack.manual_offset((UL, UR, BR))\n",
    "\n",
    "\n",
    "UL = (174.5, 171.0)\n",
    "UR = (260.5, 170.0)\n",
    "BR = (260.5, 114.0)\n",
    "stocks.manual_offset((UL, UR, BR))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1c08909c",
   "metadata": {},
   "source": [
    "You can notice that the *tiprack* and the *samples* labware have a `manualOffset()` applied to them. This is to ensure that the labware coordinates are as precise as we can. The manual offset is **labware** and **slot** dependent, so you will need to run it prior to do so. You can find more information on how to run this in the `Science Jubilee` repository/documentation"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0a923e9c",
   "metadata": {},
   "source": [
    "This next "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 271,
   "id": "544e3693",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ------------- Stocks ------------\n",
    "stock_1 = stocks[0].bottom(+5)\n",
    "stock_2 = stocks[1].bottom(+5)\n",
    "stock_3 = stocks[2].bottom(+5)\n",
    "stock_4 = stocks[3].bottom(+5)\n",
    "stock_5 = stocks[4].bottom(+5)\n",
    "stock_6 = stocks[4].bottom(+5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 272,
   "id": "419a88b6-4125-40bc-b411-2e5d194c5ee1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3)"
      ]
     },
     "execution_count": 272,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stock_1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 273,
   "id": "744d96ff-3242-4de8-8024-ff9bd1a3d0c3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'0': ((29.4, 82.1), (127, 82.1), (127, 19.2))}"
      ]
     },
     "execution_count": 273,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tiprack.manualOffset"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1c07011c",
   "metadata": {},
   "source": [
    "### Tool import and set up\n",
    "\n",
    "Once again we will need to load all our tools onto our machine both *physically* and *digitally* . \n",
    "\n",
    "To learn how to load the tools *physically*, you can find more information and resources in the `Science_Jubilee` [documentation](https://machineagency.github.io/science_jubilee/building/building_tools.html#building-tools)\n",
    "\n",
    "Each tool will at minimum require a `tool_index`, an integer, and a `tool_name`. These should be the same as the ones defined in the machine's `config.g` file. \n",
    "Some tools will also required further information. You can defined these individually or in a config file for easier tool load. "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "363b8f5d",
   "metadata": {},
   "source": [
    "**Pipette Tool**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 274,
   "id": "ed0510c0",
   "metadata": {},
   "outputs": [],
   "source": [
    "P300 = Pipette.Pipette.from_config(1, 'Pipette', 'P300_config.json')\n",
    "jubilee.load_tool(P300)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ff277a9e",
   "metadata": {},
   "source": [
    "Even though you will be able to use te pipette after these two single lines, you can also associate its `tiprack` to the tool, as well as define a `trash` location. This will just make the code more clean."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 275,
   "id": "33405bec-7810-41ab-8c2d-343b0e6c6ae2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-102.0"
      ]
     },
     "execution_count": 275,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "P300.tool_offset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 276,
   "id": "7bbeb5e9",
   "metadata": {},
   "outputs": [],
   "source": [
    "P300.add_tiprack(tiprack)\n",
    "P300.trash = trash[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "05b5dee7-c0fd-4889-a607-cf576fb09592",
   "metadata": {},
   "source": [
    "## Load experiment definition files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 237,
   "id": "96ee6f62-d9fe-4dbe-8864-9734e122184f",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "experiment_def = pd.read_csv('Drop Casting1(Hoja1).csv', sep=';')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 238,
   "id": "0984b593-f66c-4f25-b32d-ccc8b777e215",
   "metadata": {},
   "outputs": [
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    Unnamed: 0  Sample UUID  Sample Name  Stock Solution UUID Stock Location  \\\n",
       "0          0.0          NaN          NaN                  NaN        stock_1   \n",
       "1          1.0          NaN          NaN                  NaN        stock_1   \n",
       "2          2.0          NaN          NaN                  NaN        stock_1   \n",
       "3          3.0          NaN          NaN                  NaN        stock_1   \n",
       "4          4.0          NaN          NaN                  NaN        stock_1   \n",
       "5          5.0          NaN          NaN                  NaN        stock_1   \n",
       "6          6.0          NaN          NaN                  NaN        stock_2   \n",
       "7          7.0          NaN          NaN                  NaN        stock_2   \n",
       "8          8.0          NaN          NaN                  NaN        stock_2   \n",
       "9          9.0          NaN          NaN                  NaN        stock_2   \n",
       "10        10.0          NaN          NaN                  NaN        stock_2   \n",
       "11        11.0          NaN          NaN                  NaN        stock_2   \n",
       "12         NaN          NaN          NaN                  NaN            NaN   \n",
       "13         NaN          NaN          NaN                  NaN            NaN   \n",
       "14         NaN          NaN          NaN                  NaN            NaN   \n",
       "15         NaN          NaN          NaN                  NaN            NaN   \n",
       "16         NaN          NaN          NaN                  NaN            NaN   \n",
       "17         NaN          NaN          NaN                  NaN            NaN   \n",
       "18         NaN          NaN          NaN                  NaN            NaN   \n",
       "19         NaN          NaN          NaN                  NaN            NaN   \n",
       "20         NaN          NaN          NaN                  NaN            NaN   \n",
       "21         NaN          NaN          NaN                  NaN            NaN   \n",
       "22         NaN          NaN          NaN                  NaN            NaN   \n",
       "23         NaN          NaN          NaN                  NaN            NaN   \n",
       "24         NaN          NaN          NaN                  NaN            NaN   \n",
       "25         NaN          NaN          NaN                  NaN            NaN   \n",
       "26         NaN          NaN          NaN                  NaN            NaN   \n",
       "27         NaN          NaN          NaN                  NaN            NaN   \n",
       "28         NaN          NaN          NaN                  NaN            NaN   \n",
       "29         NaN          NaN          NaN                  NaN            NaN   \n",
       "30         NaN          NaN          NaN                  NaN            NaN   \n",
       "31         NaN          NaN          NaN                  NaN            NaN   \n",
       "32         NaN          NaN          NaN                  NaN            NaN   \n",
       "33         NaN          NaN          NaN                  NaN            NaN   \n",
       "34         NaN          NaN          NaN                  NaN            NaN   \n",
       "35         NaN          NaN          NaN                  NaN            NaN   \n",
       "36         NaN          NaN          NaN                  NaN            NaN   \n",
       "37         NaN          NaN          NaN                  NaN            NaN   \n",
       "38         NaN          NaN          NaN                  NaN            NaN   \n",
       "39         NaN          NaN          NaN                  NaN            NaN   \n",
       "40         NaN          NaN          NaN                  NaN            NaN   \n",
       "41         NaN          NaN          NaN                  NaN            NaN   \n",
       "42         NaN          NaN          NaN                  NaN            NaN   \n",
       "43         NaN          NaN          NaN                  NaN            NaN   \n",
       "44         NaN          NaN          NaN                  NaN            NaN   \n",
       "45         NaN          NaN          NaN                  NaN            NaN   \n",
       "46         NaN          NaN          NaN                  NaN            NaN   \n",
       "47         NaN          NaN          NaN                  NaN            NaN   \n",
       "\n",
       "    Volume dispensed [uL]  Dispense offset from center X [mm]  \\\n",
       "0                   200.0                                 2.0   \n",
       "1                   200.0                                 1.5   \n",
       "2                   200.0                                 1.0   \n",
       "3                   200.0                                 2.0   \n",
       "4                   200.0                                 1.5   \n",
       "5                   200.0                                 1.0   \n",
       "6                   200.0                                 2.0   \n",
       "7                   200.0                                 1.5   \n",
       "8                   200.0                                 1.0   \n",
       "9                   200.0                                 2.0   \n",
       "10                  200.0                                 1.5   \n",
       "11                  200.0                                 1.0   \n",
       "12                    NaN                                 NaN   \n",
       "13                    NaN                                 NaN   \n",
       "14                    NaN                                 NaN   \n",
       "15                    NaN                                 NaN   \n",
       "16                    NaN                                 NaN   \n",
       "17                    NaN                                 NaN   \n",
       "18                    NaN                                 NaN   \n",
       "19                    NaN                                 NaN   \n",
       "20                    NaN                                 NaN   \n",
       "21                    NaN                                 NaN   \n",
       "22                    NaN                                 NaN   \n",
       "23                    NaN                                 NaN   \n",
       "24                    NaN                                 NaN   \n",
       "25                    NaN                                 NaN   \n",
       "26                    NaN                                 NaN   \n",
       "27                    NaN                                 NaN   \n",
       "28                    NaN                                 NaN   \n",
       "29                    NaN                                 NaN   \n",
       "30                    NaN                                 NaN   \n",
       "31                    NaN                                 NaN   \n",
       "32                    NaN                                 NaN   \n",
       "33                    NaN                                 NaN   \n",
       "34                    NaN                                 NaN   \n",
       "35                    NaN                                 NaN   \n",
       "36                    NaN                                 NaN   \n",
       "37                    NaN                                 NaN   \n",
       "38                    NaN                                 NaN   \n",
       "39                    NaN                                 NaN   \n",
       "40                    NaN                                 NaN   \n",
       "41                    NaN                                 NaN   \n",
       "42                    NaN                                 NaN   \n",
       "43                    NaN                                 NaN   \n",
       "44                    NaN                                 NaN   \n",
       "45                    NaN                                 NaN   \n",
       "46                    NaN                                 NaN   \n",
       "47                    NaN                                 NaN   \n",
       "\n",
       "    Dispense offset from center Y [mm]  Dispense rate [uL/S]  \n",
       "0                                  2.0                 500.0  \n",
       "1                                  1.5                 500.0  \n",
       "2                                  1.0                 500.0  \n",
       "3                                  2.0                1000.0  \n",
       "4                                  1.5                1000.0  \n",
       "5                                  1.0                1000.0  \n",
       "6                                  2.0                 500.0  \n",
       "7                                  1.5                 500.0  \n",
       "8                                  1.0                 500.0  \n",
       "9                                  2.0                1000.0  \n",
       "10                                 1.5                1000.0  \n",
       "11                                 1.0                1000.0  \n",
       "12                                 NaN                   NaN  \n",
       "13                                 NaN                   NaN  \n",
       "14                                 NaN                   NaN  \n",
       "15                                 NaN                   NaN  \n",
       "16                                 NaN                   NaN  \n",
       "17                                 NaN                   NaN  \n",
       "18                                 NaN                   NaN  \n",
       "19                                 NaN                   NaN  \n",
       "20                                 NaN                   NaN  \n",
       "21                                 NaN                   NaN  \n",
       "22                                 NaN                   NaN  \n",
       "23                                 NaN                   NaN  \n",
       "24                                 NaN                   NaN  \n",
       "25                                 NaN                   NaN  \n",
       "26                                 NaN                   NaN  \n",
       "27                                 NaN                   NaN  \n",
       "28                                 NaN                   NaN  \n",
       "29                                 NaN                   NaN  \n",
       "30                                 NaN                   NaN  \n",
       "31                                 NaN                   NaN  \n",
       "32                                 NaN                   NaN  \n",
       "33                                 NaN                   NaN  \n",
       "34                                 NaN                   NaN  \n",
       "35                                 NaN                   NaN  \n",
       "36                                 NaN                   NaN  \n",
       "37                                 NaN                   NaN  \n",
       "38                                 NaN                   NaN  \n",
       "39                                 NaN                   NaN  \n",
       "40                                 NaN                   NaN  \n",
       "41                                 NaN                   NaN  \n",
       "42                                 NaN                   NaN  \n",
       "43                                 NaN                   NaN  \n",
       "44                                 NaN                   NaN  \n",
       "45                                 NaN                   NaN  \n",
       "46                                 NaN                   NaN  \n",
       "47                                 NaN                   NaN  "
      ]
     },
     "execution_count": 238,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "experiment_def"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 239,
   "id": "cad13cb6-0e99-49e7-9e7b-368657247fdf",
   "metadata": {},
   "outputs": [],
   "source": [
    "### write wrapper code to get sample values extracted from dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 240,
   "id": "6d5aae7f-d60f-4e87-89f8-35b0d9a58f94",
   "metadata": {},
   "outputs": [],
   "source": [
    "stocks = {\n",
    "    'stock_1': stock_1,\n",
    "    'stock_2': stock_2,\n",
    "    'stock_3': stock_3,\n",
    "    'stock_4': stock_4,\n",
    "    'stock_5': stock_5,\n",
    "    'stock_6': stock_6\n",
    "}\n",
    "\n",
    "samples = [\n",
    "    {\n",
    "        'stock1': stocks.get(row['Stock Location 1'], None),\n",
    "        'stock2': stocks.get(row['Stock Location 2'], None),\n",
    "        'volume1': row['Volume 1 dispensed [uL]'],\n",
    "        'volume2': row['Volume 2 dispensed [uL]'],\n",
    "        'volume_film': row['Volume Film dispensed [uL]'],\n",
    "        'dispense_offset': (\n",
    "            float(row['Dispense offset from center X [mm]'].replace(',', '.')) if pd.notnull(row['Dispense offset from center X [mm]']) else None,\n",
    "            float(row['Dispense offset from center Y [mm]'].replace(',', '.')) if pd.notnull(row['Dispense offset from center Y [mm]']) else None\n",
    "        ),\n",
    "        'dispense_rate': row['Dispense rate [uL/S]']\n",
    "    }\n",
    "    for _, row in experiment_def.iterrows()\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 241,
   "id": "96e6f683-9b04-4821-9ba3-80ded25101f6",
   "metadata": {},
   "outputs": [],
   "source": [
    "stock_location = stock_1\n",
    "volume = 200\n",
    "dispense_offset = (2,2)\n",
    "dispense_rate = 20\n",
    "\n",
    "sample_1 = {'stock':stock_1, 'volume':volume, 'dispense_offset':dispense_offset, 'dispense_rate':dispense_rate}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 242,
   "id": "ec6ee9f1-b0f7-4f6e-b1dc-ba0e6402721d",
   "metadata": {},
   "outputs": [],
   "source": [
    "for i, sample in enumerate(samples):\n",
    "    sample['location'] = sample_wellplate[i]\n",
    "    \n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "09d4d5ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "for i, sample in enumerate(samples):\n",
    "    sample['location_mixing'] = mixing_wellplate[i]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10310e8a-00a7-403b-b2a9-4e6013503c4f",
   "metadata": {},
   "source": [
    "## Run sample preparation experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 243,
   "id": "efdc189d-63d5-44c8-b6fd-610a95942b00",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'stock': Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (2.0, 2.0),\n",
       "  'dispense_rate': 500.0,\n",
       "  'location': Well A1 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.5, 1.5),\n",
       "  'dispense_rate': 500.0,\n",
       "  'location': Well A2 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.0, 1.0),\n",
       "  'dispense_rate': 500.0,\n",
       "  'location': Well A3 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (2.0, 2.0),\n",
       "  'dispense_rate': 1000.0,\n",
       "  'location': Well A4 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.5, 1.5),\n",
       "  'dispense_rate': 1000.0,\n",
       "  'location': Well A5 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(174.5, 171.0, 12.5), labware=Well A1 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.0, 1.0),\n",
       "  'dispense_rate': 1000.0,\n",
       "  'location': Well A6 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(203.16812010181744, 170.8333305167096, 12.5), labware=Well A2 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (2.0, 2.0),\n",
       "  'dispense_rate': 500.0,\n",
       "  'location': Well A7 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(203.16812010181744, 170.8333305167096, 12.5), labware=Well A2 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.5, 1.5),\n",
       "  'dispense_rate': 500.0,\n",
       "  'location': Well A8 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(203.16812010181744, 170.8333305167096, 12.5), labware=Well A2 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.0, 1.0),\n",
       "  'dispense_rate': 500.0,\n",
       "  'location': Well B1 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(203.16812010181744, 170.8333305167096, 12.5), labware=Well A2 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (2.0, 2.0),\n",
       "  'dispense_rate': 1000.0,\n",
       "  'location': Well B2 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(203.16812010181744, 170.8333305167096, 12.5), labware=Well A2 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.5, 1.5),\n",
       "  'dispense_rate': 1000.0,\n",
       "  'location': Well B3 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': Location(point=(203.16812010181744, 170.8333305167096, 12.5), labware=Well A2 form 20mLscintillation 12 Well Plate 18000 µL on slot 3),\n",
       "  'volume': 200.0,\n",
       "  'dispense_offset': (1.0, 1.0),\n",
       "  'dispense_rate': 1000.0,\n",
       "  'location': Well B4 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well B5 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well B6 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well B7 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well B8 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C1 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C2 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C3 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C4 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C5 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C6 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C7 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well C8 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D1 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D2 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D3 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D4 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D5 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D6 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D7 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well D8 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E1 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E2 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E3 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E4 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E5 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E6 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E7 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well E8 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F1 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F2 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F3 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F4 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F5 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F6 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F7 form - 48 Well Plate 600 µL on slot 2},\n",
       " {'stock': None,\n",
       "  'volume': nan,\n",
       "  'dispense_offset': (nan, nan),\n",
       "  'dispense_rate': nan,\n",
       "  'location': Well F8 form - 48 Well Plate 600 µL on slot 2}]"
      ]
     },
     "execution_count": 243,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 213,
   "id": "b1fd434b-645a-4c27-8410-1cc8897c6621",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-102.0"
      ]
     },
     "execution_count": 213,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "P300.tool_offset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f61f5c15",
   "metadata": {},
   "outputs": [],
   "source": [
    "jubilee.pickup_tool(P300)\n",
    "\n",
    "stock_tips = {\n",
    "    'stock_1': None,\n",
    "    'stock_2': None,\n",
    "    'stock_3': None\n",
    "}\n",
    "\n",
    "mixing_positions = {}\n",
    "\n",
    "for sample in samples:\n",
    "    solution_1 = sample['stock1']\n",
    "    solution_2 = sample['stock2']\n",
    "    volume_1 = sample['volume1']\n",
    "    volume_2 = sample['volume2']\n",
    "    volume_film = sample['volume_film']\n",
    "    dispense_offset = sample['dispense_offset']\n",
    "    dispense_rate = sample['dispense_rate']\n",
    "    location = sample['location']\n",
    "    location_mixing = sample['location_mixing']\n",
    "    location.x += dispense_offset[0]\n",
    "    location.y += dispense_offset[1]\n",
    "    location.bottom(+20)\n",
    "\n",
    "    key = (solution_1, solution_2, volume_1, volume_2)\n",
    "\n",
    "    if key in mixing_positions:\n",
    "        location_mixing = mixing_positions[key]\n",
    "        next_clean_tip = P300.next_tip()\n",
    "        P300.pickup_tip(next_clean_tip)\n",
    "    else:\n",
    "        mixing_positions[key] = location_mixing\n",
    "\n",
    "        if solution_1 == 'stock_1' and stock_tips['stock_1'] is None:\n",
    "            next_clean_tip = P300.next_tip()\n",
    "            P300.pickup_tip(next_clean_tip)\n",
    "            P300.assign_tip_to_stock(next_clean_tip, 'stock_1')\n",
    "            stock_tips['stock_1'] = next_clean_tip\n",
    "        elif solution_1 == 'stock_2' and stock_tips['stock_2'] is None:\n",
    "            next_clean_tip = P300.next_tip()\n",
    "            P300.pickup_tip(next_clean_tip)\n",
    "            P300.assign_tip_to_stock(next_clean_tip, 'stock_2')\n",
    "            stock_tips['stock_2'] = next_clean_tip\n",
    "        elif solution_1 == 'stock_3' and stock_tips['stock_3'] is None:\n",
    "            next_clean_tip = P300.next_tip()\n",
    "            P300.pickup_tip(next_clean_tip)\n",
    "            P300.assign_tip_to_stock(next_clean_tip, 'stock_3')\n",
    "            stock_tips['stock_3'] = next_clean_tip\n",
    "        else:\n",
    "            P300.pickup_tip(stock_tips[solution_1])\n",
    "\n",
    "        P300.aspirate(volume_1, solution_1)\n",
    "        P300.dispense(volume_1, location_mixig)\n",
    "        P300.return_tip()\n",
    "        next_clean_tip = P300.next_tip()\n",
    "        P300.pickup_tip(next_clean_tip)\n",
    "        P300.aspirate(volume_2, solution_2)\n",
    "        P300.dispense(volume_2, location_mixig)\n",
    "\n",
    "        for _ in range(3):\n",
    "            P300.aspirate(volume_2, location_mixing)\n",
    "            P300.dispense(volume_2, location_mixing)\n",
    "\n",
    "    P300.aspirate(volume_film, location_mixing)\n",
    "    P300.dispense(volume_film, location, s=dispense_rate)\n",
    "    P300.drop_tip()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "id": "ab627263-5288-45a9-8c68-9675dc321fd7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1"
      ]
     },
     "execution_count": 58,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "P300.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "id": "a5ce70b6-cdc7-4887-ac65-106a562f7ceb",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-102.0"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "P300.tool_offset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 297,
   "id": "387e75d0-28a5-42f7-85ea-67f5c2f064ff",
   "metadata": {},
   "outputs": [],
   "source": [
    "jubilee.park_tool()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 280,
   "id": "f7cbc8c1-8dcb-4edd-981a-1eaf0ea331a7",
   "metadata": {},
   "outputs": [],
   "source": [
    "jubilee.pickup_tool(P300)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 295,
   "id": "efb1bc02-db96-4830-97ae-094fd37f4a87",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Location(point=(41.2, 178.76999999999998, 22.41), labware=Well A1 form Falcon 48 Well Plate 1500 µL on slot 2)"
      ]
     },
     "execution_count": 295,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stock = stock_1\n",
    "volume = 200\n",
    "dispense_offset = (0,0)\n",
    "dispense_rate = 1000\n",
    "location = sample_wellplate[0]\n",
    "\n",
    "location.x = location.x + dispense_offset[0]\n",
    "location.y = location.y + dispense_offset[1]\n",
    "location.bottom(+20)\n",
    "\n",
    "#convert dispense rate into mL/minute"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 296,
   "id": "d2613555-b22e-418e-b2b4-9e1bc7949f55",
   "metadata": {},
   "outputs": [],
   "source": [
    "P300.pickup_tip()\n",
    "P300.aspirate(volume, stock)\n",
    "\n",
    "P300.dispense(volume, location, s = dispense_rate)\n",
    "P300.drop_tip()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 221,
   "id": "dad5645e-f012-4a33-9ae3-68dda3291ccb",
   "metadata": {},
   "outputs": [],
   "source": [
    "P300.drop_tip()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 203,
   "id": "15636507-fd48-4990-bc41-b54526430972",
   "metadata": {},
   "outputs": [
    {
     "ename": "ToolStateError",
     "evalue": "Error: No tip is attached. Cannot complete this action",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mToolStateError\u001b[0m                            Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[203], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mP300\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdispense\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvolume\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlocation\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdispense_rate\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/Code/science-jubilee/src/science_jubilee/tools/Tool.py:49\u001b[0m, in \u001b[0;36mrequires_active_tool.<locals>.wrapper\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     45\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m ToolStateError(\n\u001b[1;32m     46\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mError: Tool \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m is not the current `Active Tool`. Cannot perform this action\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     47\u001b[0m     )\n\u001b[1;32m     48\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m---> 49\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/Code/science-jubilee/src/science_jubilee/tools/Pipette.py:23\u001b[0m, in \u001b[0;36mtip_check.<locals>.wrapper\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     21\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     22\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhas_tip \u001b[38;5;241m==\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m:\n\u001b[0;32m---> 23\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m ToolStateError(\n\u001b[1;32m     24\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mError: No tip is attached. Cannot complete this action\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     25\u001b[0m         )\n\u001b[1;32m     26\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m     27\u001b[0m         func(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
      "\u001b[0;31mToolStateError\u001b[0m: Error: No tip is attached. Cannot complete this action"
     ]
    }
   ],
   "source": [
    "P300.dispense(volume, location, s = dispense_rate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2ebb7779-2150-4b3d-a283-0810430b07f2",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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